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MetabolomicsMetabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorecta...
2021-10-12 | MTBLS2130 | MetaboLights
MetabolomicsMass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids

Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies,...

2023-05-23 | MTBLS7565 | MetaboLights
MetabolomicsATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation

The induction of endoplasmic reticulum unfolded protein responses (UPRER) contributes to cancer development and progression. We recently linked microbiota-related triggers to the tumor-promoting role of signal transducer activating transcription factor 6 (ATF6) in the colon. Here we substantiate ...

2025-07-02 | MTBLS7387 | MetaboLights
TranscriptomicsTranscriptomic profiling of patient-derived endometrial cancer organoids (Berg HF)
Patient-derived endometrial cancer organoids. The data was used to compare gene expression profile between organoids, and to explore whether an organoid-derived gene signature could predict disease outcomes in independent patient cohorts.
ORGANISM(S): Homo sapiens 
2021-07-16 | E-MTAB-10664 | biostudies-arrayexpress
TranscriptomicsHuman patient tumor-derived organoid characterization from bladder cancer patients that did not respond to chemotherapy
A total of 3 independently derived organoids were compared to patient tumor samples and patient normal samples to determine if the tumor-derived organoids represent the genomic landscape of the tumor from which they were derived.
ORGANISM(S): Homo sapiens 
2023-01-02 | E-MTAB-10353 | biostudies-arrayexpress
ProteomicsPersonalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer.
We performed quantitative mass spectrometry based proteomic analysis and comparative transcriptomics analysis of 7 individual patient-derived human colorectal tumor and healthy organoids, the latter acquired from adjacent healthy tissue.
ORGANISM(S): Homo sapiens (Human) 
2017-01-16 | PXD004149 | Pride
Proteomics Organoids Colon cancer 
ProteomicsMulti-omics of colon tumor progression organoids reveals putative mediators of colorectal cancer metastasis
The development of metastasis severely reduces the life expectancy of patients with colorectal cancer (CRC). Loss of SMAD4 is a key event in late-stage CRC resulting in the progression to metastatic CRC in 10-30% of the cases. However, the biological processes and underlying molecular mechanisms tha...
ORGANISM(S): Homo sapiens (Human) 
2022-12-11 | PXD036441 | Pride
Whole-cell proteomics Secretomics Colon cancer Smad4 Metastasis 
TranscriptomicsRNA-seq of retinal organoids differentiated from hESCs carrying mutations in the RB1 gene
hESC lines carrying deleterious mutations in the RB1 gene in heterozygous and homozygous state were generated by genome-editing based on CRISPR/Cas9. Parental cell line and genome-edited cell lines were differentiated into retinal organoids for 152 days based on the Protocol published by Döpper et a...
ORGANISM(S): Homo sapiens 
2022-05-10 | E-MTAB-10331 | biostudies-arrayexpress
TranscriptomicsscRNAseq datasets of human brain organoids generated for the manuscript "Morphodynamics of human early brain organoids
Here we have provided scRNAseq datasets of unguided human brain organoids. The organoids were sequenced as a 1) Timecourse, 2) With different extracellular matrix treatments, 3) chemical treatment and 4) from organoids ere generated with a gene knockout cell line. Brain organoids enable the mechanis...
ORGANISM(S): Homo sapiens 
2025-04-30 | E-MTAB-15057 | biostudies-arrayexpress
ProteomicsImmunopeptidome of Renal Cell Carcinoma (RCC) and Bladder Cancer (BC) Patient-Derived Tumor Organoids (PDTOs)
Patient-Derived Tumor Organoids (PDTOs) have emerged as physiologically relevant systems, retaining genomic and phenotypic features of patient tumors and enabling drug response prediction. Here, we established a patient-specific pipeline to evaluate precision immunotherapy in Renal Cell Carcinoma (R...
ORGANISM(S): Homo sapiens (Human) 
2026-08-24 | PXD068567 | Pride
Ligandome Pdtos Mhc Hla-i Dda Immunopeptidomics Hla Immunopeptidome Ligandomics Patient-derived tumor organoids Renal cell carcinoma Rcc Timstof scp Mhc-i Bladder cancer 
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